Re: [gmx-users] Xe atom

2013-07-11 Thread Divya Sunil
ok thank you very much. i will try and get back to u regards divya On 11 July 2013 14:26, Dr. Vitaly Chaban wrote: > Indeed. > > > So, go to your main topology file and define a new atom type "Xe" under an > appropriate section. Then just add sigma and epsilon in the non-bonded > section and y

Re: [gmx-users] Xe atom

2013-07-11 Thread Dr. Vitaly Chaban
Indeed. So, go to your main topology file and define a new atom type "Xe" under an appropriate section. Then just add sigma and epsilon in the non-bonded section and you are ready to explore the binding. Dr. Vitaly V. Chaban On Wed, Jul 10, 2013 at 12:04 PM, Divya Sunil wrote: > ya.. but t

Re: [gmx-users] Xe atom

2013-07-10 Thread Divya Sunil
ya.. but there is experimental data to confirm the presence. can you help me to solve this problem On 9 July 2013 11:54, Dr. Vitaly Chaban wrote: > Is this, http://en.wikipedia.org/wiki/Xenon, your "Xe" ? If so, it will > obviously not sit in the binding site > > > Dr. Vitaly V. Chaban > >

Re: [gmx-users] Xe atom

2013-07-09 Thread Dr. Vitaly Chaban
Is this, http://en.wikipedia.org/wiki/Xenon, your "Xe" ? If so, it will obviously not sit in the binding site Dr. Vitaly V. Chaban On Tue, Jul 9, 2013 at 10:39 AM, Divya Sunil wrote: > thanks for the reply.. I am planning to place Xe in the protein binding > site ( just like a metal atom).

Re: [gmx-users] Xe atom

2013-07-09 Thread Divya Sunil
thanks for the reply.. I am planning to place Xe in the protein binding site ( just like a metal atom). I made a topology file with xe charge and mass. I have two options to implement the simulation. 1. like protein-ligand simulation. 2. replacing a number of solvent (water) molecules with xe in th

Re: [gmx-users] Xe atom

2013-07-08 Thread Dr. Vitaly Chaban
I am a too curious person not to ask WHY Xe is of interest in connection with the protein..? Dr. Vitaly V. Chaban On Mon, Jul 8, 2013 at 6:45 PM, Justin Lemkul wrote: > > > On 7/8/13 9:21 AM, divyasunil wrote: > >> Hello, >> >> Please help me to add Xe atom to GROMOS96 53a6 force field. I nee

Re: [gmx-users] Xe atom

2013-07-08 Thread Justin Lemkul
On 7/8/13 9:21 AM, divyasunil wrote: Hello, Please help me to add Xe atom to GROMOS96 53a6 force field. I need to carry out a protein-Xe simulation . I tried myself but failed. Parameterization is an expert topic and requires considerable time and effort. If there are existing parameters t

[gmx-users] Xe atom

2013-07-08 Thread divyasunil
Hello, Please help me to add Xe atom to GROMOS96 53a6 force field. I need to carry out a protein-Xe simulation . I tried myself but failed. Thanks and Regards Divya -- View this message in context: http://gromacs.5086.x6.nabble.com/Xe-atom-tp5009650.html Sent from the GROMACS Users Forum ma